HPCwire: NanoHUB: Gateway to Nanoscience

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March 17, 2006

NanoHUB: Gateway to Nanoscience

The nanoHUB is a Web-based initiative spearheaded by the NSF's Network for Computational Nanotechnology (NCN). Its purpose is to serve as a resource for research and education in the areas of nanoelectronics, nano-electromechanical systems (NEMS), and their application to nano-biosystems. The NCN has a mission to connect theory, experiment, and computation in a way that makes a difference to the future of nanotechnology. While addressing challenges in nanotechnology NCN researchers produce new algorithms, approaches, and software tools with capabilities not yet available commercially. As part of the NSF's infrastructure for the National Nanotechnology Initiative, the NCN engages the community through workshops and seminars and novel educational resources. The nanoHUB is a source of on-line resources including a unique web-based computational user facility that puts research-grade software in the hands users across the globe.

The nanoHUB infrastructure is in the process of being redesigned as a gateway into the TeraGrid (for more information on how the nanoHUB is taking on its new role as a TeraGrid-based science gateway, look for the article in the upcoming issue of GRIDtoday, http://www.gridtoday.com/gridtoday.html).

The research tools that the nanoHUB will be making available in the near future focus on three areas of nanoscience: nanoelectronics, nanomechanics, and bionanointerface -- which examines the ways in which electrons interface to biological systems. Deployment of these applications, geared toward researchers experienced in computational science, is anticipated within the next six months. Gerhard Klimeck, technical director of the NCN and professor of electrical and computer engineering at Purdue University, is planning to make these applications available via the nanoHUB.

Klimeck, himself, is one of the principal developers of NEMO3D, an application that performs nanoelectric modeling of quantum dots -- nanostructures that, while consisting of large numbers of atoms, behave like artificial atoms in their ability to confine a number of electrons to a small space. The size of a typical quantum dot is around 10 nanometers, or 100 times the size of an atom. Klimeck describes a quantum dot as a kind of "little laboratory where you can study a quantum mechanical system, but large enough to extract information out of that system."

By using NEMO3D to calculate the eigenvalues and eigenvectors in the quantum dot's closed system, Klimeck is able to compute the orbits of individual electrons within the dot. Recently, using NEMO3D on NCSA's TeraGrid Itanium cluster, Mercury, Klimeck and his group modeled the largest quantum dot simulation ever, consisting of 21 million atoms. Because NEMO3D is computationally intensive -- requiring 200,000 service units or more to model even a small quantum dot -- Klimeck sees it as precisely the kind of application that could best exploit the enormous computing resources the TeraGrid makes available.

Another such prospective application for the nanoHUB is BioMOCA, developed by the computational electronics group of Umberto Ravaioli, an engineering professor at UIUC and member of NCN. BioMOCA, a Monte Carlo solver for biological nanodevices, is currently being used to simulate electrolyte conduction in ionic channels in three dimensions.

"BioMOCA has been developed by adapting our framework utilized for semiconductor devices and it is intended to complement the accurate but time consuming molecular dynamics simulations used in computational biophysics," said Ravaioli.

In contrast to the vast number of atoms represented in a quantum dot, these Monte Carlo ion channel simulations typically involve only a small number of particles (ions) since water molecules are introduced implicitly as a continuum. However, applications need to run for very long times to resolve biological current flow phenomena which are much slower than in electronics devices, resulting in just as compute-intensive simulations. Ravaioli hopes that this work will facilitate interdisciplinary collaboration between engineers and biologists, by providing a tool that delivers a system description of device-like biological functions. Like NEMO3D, BioMOCA is currently being developed with NCSA support, in this case, as part of NCSA's Strategic Applications Program, which provides Ravaioli with large-scale computational resources and crucial assistance from NCSA staff.

For more information about nanoHUB, visit http://www.nanohub.org/.

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Source: National Center for Supercomputing Applications

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